/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.algorithms.utils.smithwaterman;

/**
 * Author: wbc
 */
public enum SWParameterSet {
    // match=1, mismatch = -1/3, gap=-(1+k/3)
    ORIGINAL_DEFAULT(new Parameters(3,-1,-4,-3)),

    /**
     * A standard set of values for NGS alignments
     */
    STANDARD_NGS(new Parameters(25, -50, -110, -6));

    protected Parameters parameters;

    SWParameterSet(final Parameters parameters) {
        if ( parameters == null ) throw new IllegalArgumentException("parameters cannot be null");

        this.parameters = parameters;
    }
}
